cobra
0.22.1
1. Global Configuration
2. Building a Model
3. Reading and Writing Models
4. Simulating with FBA
5. Simulating Deletions
6. Production envelopes
7. Flux sampling
8. Loopless FBA
9. Consistency testing
10. Gapfillling
11. Growth media
12. Solvers
13. Tailored constraints, variables and objectives
14. Dynamic Flux Balance Analysis (dFBA) in COBRApy
15. Using the COBRA toolbox with cobrapy
16. FAQ
17. API Reference
cobra
Docs
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Index
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Index
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Z
_
__add__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.formula.Formula method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__author__ (in module cobra)
__build_problem() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
__call__() (cobra.core.singleton.Singleton method)
(cobra.util.context.HistoryManager method)
(cobra.util.HistoryManager method)
__contains__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__copy__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Reaction method)
__deepcopy__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__delitem__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__delslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__dir__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__enter__() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
(cobra.util.process_pool.ProcessPool method)
(cobra.util.ProcessPool method)
__exit__() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
(cobra.util.process_pool.ProcessPool method)
(cobra.util.ProcessPool method)
__getattr__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
(cobra.util.process_pool.ProcessPool method)
(cobra.util.ProcessPool method)
__getitem__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.LegacySolution method)
(cobra.core.Solution method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.DictList method)
(cobra.flux_analysis.deletion.KnockoutAccessor method)
(cobra.Solution method)
(cobra.util.AutoVivification method)
(cobra.util.util.AutoVivification method)
__getslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__getstate__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Species method)
(cobra.core.species.Species method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Object method)
(cobra.sampling.optgp.OptGPSampler method)
(cobra.sampling.OptGPSampler method)
(cobra.Species method)
__iadd__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__imul__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__isub__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Reaction method)
__len__() (cobra.core.Group method)
(cobra.core.group.Group method)
__mul__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__radd__ (cobra.core.Reaction attribute)
(cobra.core.reaction.Reaction attribute)
(cobra.Reaction attribute)
__reduce__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__repr__() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
(cobra.core.LegacySolution method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Solution method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.Object method)
(cobra.Solution method)
__setitem__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__setslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__setstate__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__single_iteration() (cobra.sampling.achr.ACHRSampler method)
(cobra.sampling.ACHRSampler method)
__str__() (cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Object method)
(cobra.Reaction method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
__sub__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Reaction method)
__version__ (in module cobra)
_add_cycle_free() (in module cobra.flux_analysis.loopless)
_add_envelope() (in module cobra.flux_analysis.phenotype_phase_plane)
_as_medium() (in module cobra.medium.minimal_medium)
_associate_gene() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
_bounds_dist() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_bracket_re (in module cobra.io.mat)
_cached_load() (in module cobra.io.web.load)
_cell() (in module cobra.io.mat)
_check() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
(in module cobra.io.mat)
(in module cobra.io.sbml)
_check_bounds() (cobra.core.Reaction static method)
(cobra.core.reaction.Reaction static method)
(cobra.Reaction static method)
_check_required() (in module cobra.io.sbml)
_check_sbml_annotations() (in module test_annotation)
_clean_up() (cobra.util.process_pool.ProcessPool method)
(cobra.util.ProcessPool method)
_clip() (in module cobra.io.sbml)
_create_bound() (in module cobra.io.sbml)
_create_parameter() (in module cobra.io.sbml)
_display_flux() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
_dissociate_gene() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
_element_lists() (in module cobra.flux_analysis.deletion)
_entities_ids() (in module cobra.flux_analysis.deletion)
_error_string() (in module cobra.io.sbml)
_escape_non_alphanum() (in module cobra.io.sbml)
_escape_str_id() (in module cobra.manipulation.modify)
_extend_nocheck() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
_f_gene() (in module cobra.io.sbml)
_f_gene_rev() (in module cobra.io.sbml)
_f_group() (in module cobra.io.sbml)
_f_group_rev() (in module cobra.io.sbml)
_f_reaction() (in module cobra.io.sbml)
_f_reaction_rev() (in module cobra.io.sbml)
_f_specie() (in module cobra.io.sbml)
_f_specie_rev() (in module cobra.io.sbml)
_fetch_model() (in module cobra.io.web.load)
_find_carbon_sources() (in module cobra.flux_analysis.phenotype_phase_plane)
_find_gene_knockout_reactions_fast() (in module cobra.test.test_manipulation.test_delete)
_find_sparse_mode() (in module cobra.flux_analysis.fastcc)
_fix_type() (in module cobra.io.dict)
_flip_coefficients() (in module cobra.flux_analysis.fastcc)
_forward_arrow_finder (in module cobra.core.reaction)
_fva_step() (in module cobra.flux_analysis.variability)
_gene_deletion() (in module cobra.flux_analysis.deletion)
_gene_deletion_worker() (in module cobra.flux_analysis.deletion)
_gene_knockout_computation() (in module cobra.test.test_manipulation.test_delete)
_GeneEscaper (class in cobra.manipulation.modify)
_generate() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
_generate_index() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
_GeneRemover (class in cobra.manipulation.delete)
_get_doc_from_filename() (in module cobra.io.sbml)
_get_growth() (in module cobra.flux_analysis.deletion)
_get_id_compartment() (in module cobra.io.mat)
_get_removed() (in module cobra.test.test_manipulation.test_delete)
_html_table() (cobra.summary.metabolite_summary.MetaboliteSummary static method)
(cobra.summary.MetaboliteSummary static method)
(cobra.summary.model_summary.ModelSummary static method)
(cobra.summary.ModelSummary static method)
_init_worker() (in module cobra.flux_analysis.deletion)
(in module cobra.flux_analysis.variability)
_instances (cobra.core.singleton.Singleton attribute)
_is_redundant() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_model_to_sbml() (in module cobra.io.sbml)
_multi_deletion() (in module cobra.flux_analysis.deletion)
_normalize_threshold() (cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
_NOT_MASS_BALANCED_TERMS (in module cobra.manipulation.validate)
_number_to_chr() (in module cobra.io.sbml)
_optimize_or_value() (in module cobra.flux_analysis.reaction)
_OPTIONAL_GENE_ATTRIBUTES (in module cobra.io.dict)
_OPTIONAL_METABOLITE_ATTRIBUTES (in module cobra.io.dict)
_OPTIONAL_MODEL_ATTRIBUTES (in module cobra.io.dict)
_OPTIONAL_REACTION_ATTRIBUTES (in module cobra.io.dict)
_ORDERED_OPTIONAL_GENE_KEYS (in module cobra.io.dict)
_ORDERED_OPTIONAL_METABOLITE_KEYS (in module cobra.io.dict)
_ORDERED_OPTIONAL_MODEL_KEYS (in module cobra.io.dict)
_ORDERED_OPTIONAL_REACTION_KEYS (in module cobra.io.dict)
_parse_annotation_info() (in module cobra.io.sbml)
_parse_annotations() (in module cobra.io.sbml)
_parse_notes_dict() (in module cobra.io.sbml)
_populate_solver() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
_progress (cobra.io.AbstractModelRepository attribute)
(cobra.io.web.abstract_model_repository.AbstractModelRepository attribute)
(cobra.io.web.AbstractModelRepository attribute)
_random_point() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_reaction_deletion() (in module cobra.flux_analysis.deletion)
_reaction_deletion_worker() (in module cobra.flux_analysis.deletion)
_reaction_elements() (in module cobra.flux_analysis.phenotype_phase_plane)
_reaction_weight() (in module cobra.flux_analysis.phenotype_phase_plane)
_Renamer (class in cobra.manipulation.modify)
_renames (in module cobra.manipulation.modify)
_replace_on_id() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
_repr_html_() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
(cobra.core.Gene method)
(cobra.core.gene.Gene method)
(cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.core.Solution method)
(cobra.core.solution.Solution method)
(cobra.Gene method)
(cobra.Metabolite method)
(cobra.Model method)
(cobra.Reaction method)
(cobra.Solution method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
_reproject() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_REQUIRED_GENE_ATTRIBUTES (in module cobra.io.dict)
_REQUIRED_METABOLITE_ATTRIBUTES (in module cobra.io.dict)
_REQUIRED_REACTION_ATTRIBUTES (in module cobra.io.dict)
_reverse_arrow_finder (in module cobra.core.reaction)
_reversible_arrow_finder (in module cobra.core.reaction)
_sbase_annotations() (in module cobra.io.sbml)
_sbase_notes_dict() (in module cobra.io.sbml)
_sbml_to_model() (in module cobra.io.sbml)
_set_default_cache_directory() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
_set_default_processes() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
_set_default_solver() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
_set_id_with_model() (cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Metabolite method)
(cobra.Object method)
(cobra.Reaction method)
_string_flux() (cobra.summary.reaction_summary.ReactionSummary method)
_string_objective() (cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
_string_table() (cobra.summary.metabolite_summary.MetaboliteSummary static method)
(cobra.summary.MetaboliteSummary static method)
(cobra.summary.model_summary.ModelSummary static method)
(cobra.summary.ModelSummary static method)
_total_components_flux() (in module cobra.flux_analysis.phenotype_phase_plane)
_total_yield() (in module cobra.flux_analysis.phenotype_phase_plane)
_underscore_re (in module cobra.io.mat)
_update_awareness() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
_update_optional() (in module cobra.io.dict)
_valid_atoms() (in module cobra.util)
(in module cobra.util.solver)
_validate() (cobra.flux_analysis.deletion.KnockoutAccessor static method)
A
AbstractModelRepository (class in cobra.io)
(class in cobra.io.web)
(class in cobra.io.web.abstract_model_repository)
achr() (in module conftest)
ACHRSampler (class in cobra.sampling)
(class in cobra.sampling.achr)
add() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
add_absolute_expression() (in module cobra.util)
(in module cobra.util.solver)
add_boundary() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_cons_vars() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_cons_vars_to_problem() (in module cobra.util)
(in module cobra.util.solver)
add_groups() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_lexicographic_constraints() (in module cobra.util)
(in module cobra.util.solver)
add_linear_obj() (in module cobra.medium.minimal_medium)
add_loopless() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.loopless)
add_lp_feasibility() (in module cobra.util)
(in module cobra.util.solver)
add_members() (cobra.core.Group method)
(cobra.core.group.Group method)
add_metabolites() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Model method)
(cobra.Reaction method)
add_mip_obj() (in module cobra.medium.minimal_medium)
add_moma() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.moma)
add_pfba() (in module cobra.flux_analysis.parsimonious)
add_reaction() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_reactions() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_room() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.room)
add_SBO() (in module cobra.manipulation)
(in module cobra.manipulation.annotate)
add_switches_and_objective() (cobra.flux_analysis.gapfilling.GapFiller method)
all_solvers (in module cobra.test.conftest)
and_or_search (in module cobra.core.reaction)
annotation() (cobra.core.Object property)
(cobra.core.object.Object property)
(cobra.Object property)
append() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
assert_optimal() (in module cobra.util)
(in module cobra.util.solver)
assess() (in module cobra.flux_analysis.reaction)
assess_component() (in module cobra.flux_analysis.reaction)
assess_precursors() (in module cobra.flux_analysis.reaction)
assess_products() (in module cobra.flux_analysis.reaction)
ast2str() (in module cobra.core.gene)
attribute() (in module test_io_order)
AutoVivification (class in cobra.util)
(class in cobra.util.util)
B
b (in module cobra.sampling.hr_sampler)
batch() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
bigg_models() (in module test_load)
BiGGModels (class in cobra.io)
(class in cobra.io.web)
(class in cobra.io.web.bigg_models_repository)
BioModels (class in cobra.io)
(class in cobra.io.web)
(class in cobra.io.web.biomodels_repository)
biomodels() (in module test_load)
BioModelsFile (class in cobra.io.web.biomodels_repository)
BioModelsFilesResponse (class in cobra.io.web.biomodels_repository)
BOUND_MINUS_INF (in module cobra.io.sbml)
BOUND_PLUS_INF (in module cobra.io.sbml)
boundary() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Model property)
(cobra.Reaction property)
bounds (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(in module cobra.sampling.hr_sampler)
bounds() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
bounds_tol (cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
build_reaction_from_string() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
build_reaction_string() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
C
cache_directory (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
cache_directory() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
cache_expiration (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
center (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
check_mass_balance() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
(in module cobra.manipulation)
(in module cobra.manipulation.validate)
check_metabolite_compartment_formula() (in module cobra.manipulation)
(in module cobra.manipulation.validate)
check_solver() (in module cobra.util)
(in module cobra.util.solver)
check_solver_status() (in module cobra.util)
(in module cobra.util.solver)
choose_solver() (in module cobra.util)
(in module cobra.util.solver)
cload (in module test_pickle)
close() (cobra.util.process_pool.ProcessPool method)
(cobra.util.ProcessPool method)
cobra (module)
cobra.core (module)
cobra.core.configuration (module)
cobra.core.dictlist (module)
cobra.core.formula (module)
cobra.core.gene (module)
cobra.core.group (module)
cobra.core.metabolite (module)
cobra.core.model (module)
cobra.core.object (module)
cobra.core.reaction (module)
cobra.core.singleton (module)
cobra.core.solution (module)
cobra.core.species (module)
cobra.exceptions (module)
cobra.flux_analysis (module)
cobra.flux_analysis.deletion (module)
cobra.flux_analysis.fastcc (module)
cobra.flux_analysis.gapfilling (module)
cobra.flux_analysis.geometric (module)
cobra.flux_analysis.helpers (module)
cobra.flux_analysis.loopless (module)
cobra.flux_analysis.moma (module)
cobra.flux_analysis.parsimonious (module)
cobra.flux_analysis.phenotype_phase_plane (module)
cobra.flux_analysis.reaction (module)
cobra.flux_analysis.room (module)
cobra.flux_analysis.variability (module)
cobra.io (module)
cobra.io.dict (module)
cobra.io.json (module)
cobra.io.mat (module)
cobra.io.sbml (module)
cobra.io.web (module)
cobra.io.web.abstract_model_repository (module)
cobra.io.web.bigg_models_repository (module)
cobra.io.web.biomodels_repository (module)
cobra.io.web.load (module)
cobra.io.yaml (module)
cobra.manipulation (module)
cobra.manipulation.annotate (module)
cobra.manipulation.delete (module)
cobra.manipulation.modify (module)
cobra.manipulation.validate (module)
cobra.medium (module)
cobra.medium.annotations (module)
cobra.medium.boundary_types (module)
cobra.medium.minimal_medium (module)
cobra.sampling (module)
cobra.sampling.achr (module)
cobra.sampling.core (module)
cobra.sampling.hr_sampler (module)
cobra.sampling.optgp (module)
cobra.sampling.sampling (module)
cobra.summary (module)
cobra.summary.metabolite_summary (module)
cobra.summary.model_summary (module)
cobra.summary.reaction_summary (module)
cobra.summary.summary (module)
cobra.test (module)
cobra.test.conftest (module)
cobra.test.test_manipulation (module)
cobra.test.test_manipulation.test_annotate (module)
cobra.test.test_manipulation.test_delete (module)
cobra.test.test_manipulation.test_modify (module)
cobra.test.test_manipulation.test_validate (module)
cobra.util (module)
cobra.util.array (module)
cobra.util.context (module)
cobra.util.process_pool (module)
cobra.util.solver (module)
cobra.util.util (module)
cobra_directory (in module cobra.test)
cobra_location (in module cobra.test)
CobraSBMLError
compare_models() (test_sbml.TestCobraIO class method)
compartment_finder (in module cobra.core.reaction)
compartment_shortlist (in module cobra.medium.annotations)
compartments() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Model property)
(cobra.Reaction property)
Components (class in cobra.util)
(class in cobra.util.solver)
config (in module cobra.core.reaction)
(in module cobra.io.sbml)
(in module test_core_reaction)
(in module test_sbml)
(in module update_pickles)
Configuration (class in cobra)
(class in cobra.core)
(class in cobra.core.configuration)
configuration (in module cobra.core.model)
(in module cobra.flux_analysis.deletion)
(in module cobra.flux_analysis.variability)
(in module cobra.io.web.load)
conftest (module)
CONS_VARS (in module cobra.util)
(in module cobra.util.solver)
constraint() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
constraint_matrices() (in module cobra.util)
(in module cobra.util.array)
constraints() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
construct_ll_test_model() (in module test_loopless)
consuming_flux (cobra.summary.metabolite_summary.MetaboliteSummary attribute)
(cobra.summary.MetaboliteSummary attribute)
copy() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.core.Species method)
(cobra.core.species.Species method)
(cobra.Model method)
(cobra.Reaction method)
(cobra.Species method)
costs (cobra.flux_analysis.gapfilling.GapFiller attribute)
create_mat_dict() (in module cobra.io.mat)
create_mat_metabolite_id() (in module cobra.io.mat)
create_stoichiometric_matrix() (in module cobra.util)
(in module cobra.util.array)
create_test_model() (in module cobra.test)
D
data_dir (in module cobra.test)
data_directory() (in module cobra.test.conftest)
delete() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
delete_model_genes() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
demands() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
description() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
dict_list() (in module test_dictlist)
DictList (class in cobra)
(class in cobra.core)
(class in cobra.core.dictlist)
double_gene_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
double_reaction_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
dress_results() (cobra.core.LegacySolution method)
(cobra.core.solution.LegacySolution method)
dummy_initializer() (in module test_process_pool)
dump() (cobra.io.yaml.MyYAML method)
E
ecoli_model (in module update_pickles)
element_re (in module cobra.core.formula)
(in module cobra.core.metabolite)
elements() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
elements_and_molecular_weights (in module cobra.core.formula)
empty_model() (in module cobra.test.conftest)
empty_once() (in module cobra.test.conftest)
equalities (in module cobra.sampling.hr_sampler)
escape_ID() (in module cobra.manipulation)
(in module cobra.manipulation.modify)
eval_gpr() (in module cobra.core.gene)
exchanges() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
excludes (in module cobra.medium.annotations)
extend() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
extend_model() (cobra.flux_analysis.gapfilling.GapFiller method)
extra_comparisons() (test_sbml.TestCobraIO class method)
F
f (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
F_GENE (in module cobra.io.sbml)
F_GENE_REV (in module cobra.io.sbml)
F_GROUP (in module cobra.io.sbml)
F_GROUP_REV (in module cobra.io.sbml)
F_REACTION (in module cobra.io.sbml)
F_REACTION_REV (in module cobra.io.sbml)
F_REPLACE (in module cobra.io.sbml)
F_SPECIE (in module cobra.io.sbml)
F_SPECIE_REV (in module cobra.io.sbml)
fastcc() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.fastcc)
feasibility_tol (cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
FeasibleButNotOptimal
figure1_model() (in module test_fastcc)
fill() (cobra.flux_analysis.gapfilling.GapFiller method)
find_blocked_reactions() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
find_boundary_types() (in module cobra.medium)
(in module cobra.medium.boundary_types)
find_essential_genes() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
find_essential_reactions() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
find_external_compartment() (in module cobra.medium)
(in module cobra.medium.boundary_types)
find_gene_knockout_reactions() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
fix_objective_as_constraint() (in module cobra.util)
(in module cobra.util.solver)
flux() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
flux_expression() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
flux_variability_analysis() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
fluxes (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
format_long_string() (in module cobra.util)
(in module cobra.util.util)
Formula (class in cobra.core.formula)
formula_weight() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
forward_variable() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
from_json() (in module cobra.io)
(in module cobra.io.json)
from_mat_struct() (in module cobra.io.mat)
from_yaml() (in module cobra.io)
(in module cobra.io.yaml)
functional() (cobra.core.Gene property)
(cobra.core.gene.Gene property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Gene property)
(cobra.Reaction property)
fva_results() (in module cobra.test.conftest)
fwd_idx (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
G
gapfill() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.gapfilling)
GapFiller (class in cobra.flux_analysis.gapfilling)
Gene (class in cobra)
(class in cobra.core)
(class in cobra.core.gene)
gene_from_dict() (in module cobra.io.dict)
gene_name_reaction_rule() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
gene_reaction_rule() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
gene_to_dict() (in module cobra.io.dict)
generate_fva_warmup() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
genes (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
genes() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
geometric_fba() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.geometric)
geometric_fba_model() (in module test_geometric)
get_associated_groups() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
get_by_any() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
get_by_id() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
get_coefficient() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
get_coefficients() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
get_compartments() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
get_compiled_gene_reaction_rules() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
get_context() (in module cobra.util)
,
[1]
(in module cobra.util.context)
get_ids() (in module test_io_order)
get_metabolite_compartments() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
get_model_from_gzip_sbml() (in module cobra.io.web.load)
get_primal_by_id (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
get_sbml() (cobra.io.AbstractModelRepository method)
(cobra.io.BiGGModels method)
(cobra.io.BioModels method)
(cobra.io.web.abstract_model_repository.AbstractModelRepository method)
(cobra.io.web.AbstractModelRepository method)
(cobra.io.web.bigg_models_repository.BiGGModels method)
(cobra.io.web.BiGGModels method)
(cobra.io.web.BioModels method)
(cobra.io.web.biomodels_repository.BioModels method)
get_solution() (in module cobra.core)
(in module cobra.core.solution)
get_solver_name() (in module cobra.util)
(in module cobra.util.solver)
gpr_clean (in module cobra.core.reaction)
GPRCleaner (class in cobra.core.gene)
Group (class in cobra.core)
(class in cobra.core.group)
groups (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
H
has_id() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
has_primals (in module cobra.util)
(in module cobra.util.solver)
HistoryManager (class in cobra.util)
(class in cobra.util.context)
homogeneous (in module cobra.sampling.hr_sampler)
HRSampler (class in cobra.sampling)
(class in cobra.sampling.hr_sampler)
I
id() (cobra.core.Object property)
(cobra.core.object.Object property)
(cobra.Object property)
index() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
indicators (cobra.flux_analysis.gapfilling.GapFiller attribute)
inequalities (in module cobra.sampling.hr_sampler)
Infeasible
insert() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
interface_to_str() (in module cobra.util)
(in module cobra.util.solver)
io_trial() (in module test_sbml)
IOTrial (in module test_sbml)
is_boundary_type() (in module cobra.medium)
(in module cobra.medium.boundary_types)
J
json_schema_v1() (in module test_json)
JSON_SPEC (in module cobra.io.json)
jsonschema (in module test_sbml)
K
keyword_re (in module cobra.core.gene)
keywords (in module cobra.core.gene)
kind() (cobra.core.Group property)
(cobra.core.group.Group property)
KIND_TYPES (cobra.core.Group attribute)
(cobra.core.group.Group attribute)
knock_out() (cobra.core.Gene method)
(cobra.core.gene.Gene method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Gene method)
(cobra.Reaction method)
KnockoutAccessor (class in cobra.flux_analysis.deletion)
L
large_model() (in module cobra.test.conftest)
large_once() (in module cobra.test.conftest)
LegacySolution (class in cobra.core)
(class in cobra.core.solution)
linear_reaction_coefficients() (in module cobra.util)
(in module cobra.util.solver)
list_attr() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
ll_test_model() (in module test_loopless)
load_json_model() (in module cobra.io)
(in module cobra.io.json)
load_matlab_model() (in module cobra.io)
(in module cobra.io.mat)
load_model() (in module cobra.io)
(in module cobra.io.web)
(in module cobra.io.web.load)
load_yaml_model() (in module cobra.io)
(in module cobra.io.yaml)
logger (in module cobra.core.model)
(in module cobra.flux_analysis.gapfilling)
(in module cobra.flux_analysis.geometric)
LOGGER (in module cobra.flux_analysis.helpers)
(in module cobra.flux_analysis.loopless)
logger (in module cobra.flux_analysis.variability)
LOGGER (in module cobra.io.sbml)
logger (in module cobra.io.web.load)
(in module cobra.medium.boundary_types)
(in module cobra.medium.minimal_medium)
(in module cobra.sampling.core)
(in module cobra.sampling.hr_sampler)
(in module cobra.summary.metabolite_summary)
(in module cobra.summary.model_summary)
(in module cobra.summary.reaction_summary)
(in module cobra.summary.summary)
(in module cobra.util)
(in module cobra.util.solver)
LOGGER (in module test_io_order)
LONG_SHORT_DIRECTION (in module cobra.io.sbml)
loopless_fva_iter() (in module cobra.flux_analysis.loopless)
loopless_solution() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.loopless)
lower_bound (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
lower_bound() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
LOWER_BOUND_ID (in module cobra.io.sbml)
lower_constraint (cobra.util.Components attribute)
(cobra.util.solver.Components attribute)
M
main (cobra.io.web.biomodels_repository.BioModelsFilesResponse attribute)
max_cache_size (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
MAX_TRIES (in module cobra.sampling.core)
medium() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
medium_model() (in module cobra.test.conftest)
members() (cobra.core.Group property)
(cobra.core.group.Group property)
merge() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
Metabolite (class in cobra)
(class in cobra.core)
(class in cobra.core.metabolite)
metabolite_from_dict() (in module cobra.io.dict)
metabolite_to_dict() (in module cobra.io.dict)
metabolites (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
metabolites() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
(in module cobra.test.conftest)
MetaboliteSummary (class in cobra.summary)
(class in cobra.summary.metabolite_summary)
mini_sbml() (in module test_load)
minimal_medium() (in module cobra.medium)
(in module cobra.medium.minimal_medium)
minimized_reverse() (in module test_io_order)
minimized_shuffle() (in module test_io_order)
minimized_sorted() (in module test_io_order)
Model (class in cobra)
(class in cobra.core)
(class in cobra.core.model)
model() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.core.Species property)
(cobra.core.species.Species property)
(cobra.Reaction property)
(cobra.Species property)
(in module cobra.test.conftest)
model_from_dict() (in module cobra.io)
(in module cobra.io.dict)
model_to_dict() (in module cobra.io)
(in module cobra.io.dict)
model_to_pymatbridge() (in module cobra.io.mat)
ModelSummary (class in cobra.summary)
(class in cobra.summary.model_summary)
moma() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.moma)
MyYAML (class in cobra.io.yaml)
N
n_samples (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
name (cobra.io.AbstractModelRepository attribute)
,
[1]
(cobra.io.BiGGModels attribute)
,
[1]
(cobra.io.BioModels attribute)
,
[1]
(cobra.io.web.abstract_model_repository.AbstractModelRepository attribute)
,
[1]
(cobra.io.web.AbstractModelRepository attribute)
,
[1]
(cobra.io.web.bigg_models_repository.BiGGModels attribute)
,
[1]
(cobra.io.web.BiGGModels attribute)
,
[1]
(cobra.io.web.BioModels attribute)
,
[1]
(cobra.io.web.biomodels_repository.BioModels attribute)
,
[1]
(cobra.io.web.biomodels_repository.BioModelsFile attribute)
normalize_cutoff() (in module cobra.flux_analysis.helpers)
nullspace (in module cobra.sampling.hr_sampler)
nullspace() (in module cobra.util)
(in module cobra.util.array)
number_start_re (in module cobra.core.gene)
O
Object (class in cobra)
(class in cobra.core)
(class in cobra.core.object)
objective() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
objective_coefficient() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
objective_direction() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
objective_value (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
opposing_model() (in module test_fastcc)
opt_solver() (in module cobra.test.conftest)
optgp() (in module test_optgp)
OptGPSampler (class in cobra.sampling)
(class in cobra.sampling.optgp)
OptimizationError
,
[1]
optimize() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
optimize_minimal_flux() (in module cobra.flux_analysis.parsimonious)
optlang_solvers (in module test_model)
(in module test_solver)
OPTLANG_TO_EXCEPTIONS_DICT (in module cobra.exceptions)
(in module cobra.util)
P
parse_composition() (cobra.core.formula.Formula method)
parse_gpr() (in module cobra.core.gene)
pattern_from_sbml (in module cobra.io.sbml)
pattern_notes (in module cobra.io.sbml)
pattern_to_sbml (in module cobra.io.sbml)
pfba() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.parsimonious)
pfba_fva_results() (in module cobra.test.conftest)
pop() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
prev (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
problem (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
Problem (in module cobra.sampling.hr_sampler)
problem() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
processes (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
ProcessPool (class in cobra.util)
(class in cobra.util.process_pool)
producing_flux (cobra.summary.metabolite_summary.MetaboliteSummary attribute)
(cobra.summary.MetaboliteSummary attribute)
production_envelope() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.phenotype_phase_plane)
products() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
prune_unused_metabolites() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
prune_unused_reactions() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
pytest (in module cobra.test)
pytest_addoption() (in module cobra.test.conftest)
Q
qp_solvers (in module cobra.util)
(in module cobra.util.solver)
QUALIFIER_TYPES (in module cobra.io.sbml)
query() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
R
raven_model() (in module test_mat)
reactants() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
Reaction (class in cobra)
(class in cobra.core)
(class in cobra.core.reaction)
reaction() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
reaction_from_dict() (in module cobra.io.dict)
reaction_to_dict() (in module cobra.io.dict)
reactions (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
reactions() (cobra.core.Species property)
(cobra.core.species.Species property)
(cobra.Species property)
ReactionSummary (class in cobra.summary.reaction_summary)
read_sbml_model() (in module cobra.io)
(in module cobra.io.sbml)
(in module cobra.test)
reduced_cost() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
reduced_costs (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
remove() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
remove_cons_vars() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
remove_cons_vars_from_problem() (in module cobra.util)
(in module cobra.util.solver)
remove_from_model() (cobra.core.Gene method)
(cobra.core.gene.Gene method)
(cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Gene method)
(cobra.Metabolite method)
(cobra.Reaction method)
remove_genes() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
remove_groups() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
remove_members() (cobra.core.Group method)
(cobra.core.group.Group method)
remove_metabolites() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
remove_reactions() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
rename_genes() (in module cobra.manipulation)
(in module cobra.manipulation.modify)
repair() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
replacements (in module cobra.core.gene)
reset() (cobra.util.context.HistoryManager method)
(cobra.util.HistoryManager method)
resettable() (in module cobra.util)
(in module cobra.util.context)
retries (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
rev_idx (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
reverse() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
reverse_id() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
reverse_variable() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
reversibility() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
room() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.room)
S
salmonella() (in module cobra.test.conftest)
same_ex() (in module test_model)
sample() (cobra.sampling.achr.ACHRSampler method)
(cobra.sampling.ACHRSampler method)
(cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
(cobra.sampling.optgp.OptGPSampler method)
(cobra.sampling.OptGPSampler method)
(in module cobra.sampling)
(in module cobra.sampling.sampling)
save_json_model() (in module cobra.io)
(in module cobra.io.json)
save_matlab_model() (in module cobra.io)
(in module cobra.io.mat)
save_yaml_model() (in module cobra.io)
(in module cobra.io.yaml)
SBML_DOT (in module cobra.io.sbml)
SBO_DEFAULT_FLUX_BOUND (in module cobra.io.sbml)
SBO_EXCHANGE_REACTION (in module cobra.io.sbml)
SBO_FBA_FRAMEWORK (in module cobra.io.sbml)
SBO_FLUX_BOUND (in module cobra.io.sbml)
sbo_terms (in module cobra.medium)
(in module cobra.medium.annotations)
scipy (in module test_mat)
scipy_sparse (in module cobra.io.mat)
secretion_flux (cobra.summary.model_summary.ModelSummary attribute)
(cobra.summary.ModelSummary attribute)
set_objective() (in module cobra.util)
(in module cobra.util.solver)
shadow_price() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
shadow_prices (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
shared_np_array() (in module cobra.sampling)
(in module cobra.sampling.hr_sampler)
SHORT_LONG_DIRECTION (in module cobra.io.sbml)
show_versions() (in module cobra)
(in module cobra.util)
(in module cobra.util.util)
single_gene_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
single_reaction_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
Singleton (class in cobra.core.singleton)
sinks() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
size (cobra.io.web.biomodels_repository.BioModelsFile attribute)
size() (cobra.util.context.HistoryManager method)
(cobra.util.HistoryManager method)
slim_optimize() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
small_model() (in module cobra.test.conftest)
Solution (class in cobra)
(class in cobra.core)
(class in cobra.core.solution)
solution (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
solved_model() (in module cobra.test.conftest)
solver (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
(in module update_pickles)
solver() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
(cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
SolverNotFound
,
[1]
solvers (in module cobra.util)
(in module cobra.util.solver)
sort() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
Species (class in cobra)
(class in cobra.core)
(class in cobra.core.species)
square() (in module test_process_pool)
stable_optlang (in module cobra.test.conftest)
(in module test_core_reaction)
(in module test_model)
(in module test_solver)
status (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
step() (in module cobra.sampling)
(in module cobra.sampling.core)
subtract_metabolites() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
Summary (class in cobra.summary)
(class in cobra.summary.summary)
summary() (cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Metabolite method)
(cobra.Model method)
(cobra.Reaction method)
summation() (in module test_process_pool)
T
template() (in module test_io_order)
test_absolute_expression() (in module test_solver)
test_achr (module)
test_achr_init_benchmark() (in module test_achr)
test_achr_sample_benchmark() (in module test_achr)
test_add() (in module test_core_reaction)
(in module test_dictlist)
test_add_boundary() (in module test_model)
test_add_boundary_context() (in module test_model)
test_add_cobra_reaction() (in module test_model)
test_add_existing_boundary() (in module test_model)
test_add_lexicographic_constraints() (in module test_solver)
test_add_loopless() (in module test_loopless)
test_add_lp_feasibility() (in module test_solver)
test_add_metabolite() (in module test_core_reaction)
(in module test_model)
test_add_metabolite_benchmark() (in module test_core_reaction)
test_add_metabolite_from_solved_model() (in module test_core_reaction)
test_add_metabolites_combine_false() (in module test_core_reaction)
test_add_metabolites_combine_true() (in module test_core_reaction)
test_add_reaction() (in module test_model)
test_add_reaction_context() (in module test_model)
test_add_reaction_from_other_model() (in module test_model)
test_add_reaction_orphans() (in module test_model)
test_add_reactions() (in module test_model)
test_add_reactions_duplicate() (in module test_model)
test_add_reactions_single_existing() (in module test_model)
test_add_remove() (in module test_solver)
test_add_remove_in_context() (in module test_solver)
test_add_remove_reaction_benchmark() (in module test_model)
test_all() (in module cobra.test)
test_all_objects_point_to_all_other_correct_objects() (in module test_model)
test_annotation (module)
test_annotation_format (module)
test_append() (in module test_dictlist)
test_apply() (in module test_process_pool)
test_apply_async() (in module test_process_pool)
test_array (module)
test_assess() (in module test_reaction)
test_autovivification() (in module test_util)
test_bad_exchange() (in module test_boundary_types)
test_batch_sampling() (in module test_achr)
(in module test_optgp)
test_bigg_access() (in module test_load)
test_biomodels_access() (in module test_load)
test_boundary_conditions() (in module test_sbml)
test_boundary_types (module)
test_bounds() (in module test_configuration)
test_bounds_setter() (in module test_core_reaction)
test_build_from_string() (in module test_core_reaction)
test_cache() (in module test_load)
test_change_bounds() (in module test_core_reaction)
test_change_id_is_reflected_in_solver() (in module test_core_reaction)
test_change_objective() (in module test_model)
,
[1]
test_change_objective_benchmark() (in module test_model)
test_change_objective_through_objective_coefficient() (in module test_model)
test_change_solver_to_cplex_and_check_copy_works() (in module test_model)
test_choose_solver() (in module test_solver)
test_close() (in module test_process_pool)
test_compartment_changes() (in module test_core_reaction)
test_compartments() (in module test_model)
test_complicated_model() (in module test_sampling)
test_configuration (module)
test_contains() (in module test_dictlist)
test_context (module)
test_context_manager() (in module test_model)
test_copy() (in module test_core_reaction)
(in module test_dictlist)
(in module test_model)
test_copy_benchmark() (in module test_model)
test_copy_benchmark_large_model() (in module test_model)
test_copy_preserves_existing_solution() (in module test_model)
test_copy_with_groups() (in module test_model)
test_core_reaction (module)
test_deepcopy() (in module test_dictlist)
(in module test_model)
test_deepcopy_benchmark() (in module test_model)
test_default_bounds() (in module test_configuration)
test_default_tolerance() (in module test_configuration)
test_deletion (module)
test_deletion_accessor() (in module test_deletion)
test_dense_matrix() (in module test_array)
test_dictlist (module)
test_dir() (in module test_dictlist)
test_double_gene_deletion() (in module test_deletion)
test_double_gene_deletion_benchmark() (in module test_deletion)
test_double_gene_knockout_bug() (in module test_deletion)
test_double_reaction_deletion() (in module test_deletion)
test_double_reaction_deletion_benchmark() (in module test_deletion)
test_envelope_multi_reaction_objective() (in module test_phenotype_phase_plane)
test_envelope_one() (in module test_phenotype_phase_plane)
test_envelope_two() (in module test_phenotype_phase_plane)
test_equality_constraint() (in module test_sampling)
test_escape_ids() (in module cobra.test.test_manipulation.test_modify)
test_essential_genes() (in module test_variability)
test_essential_reactions() (in module test_variability)
test_exchange_reactions() (in module test_model)
test_extend() (in module test_dictlist)
test_fail_non_linear_reaction_coefficients() (in module test_solver)
test_fastcc (module)
test_fastcc_against_fva_nonblocked_rxns() (in module test_fastcc)
test_fastcc_benchmark() (in module test_fastcc)
test_fdp_production_with_fva() (in module test_metabolite_summary)
test_figure1() (in module test_fastcc)
test_filehandle() (in module test_sbml)
test_find_blocked_reactions() (in module test_variability)
test_find_blocked_reactions_solver_none() (in module test_variability)
test_find_boundary_types_demand() (in module test_boundary_types)
test_find_boundary_types_exchange() (in module test_boundary_types)
test_find_boundary_types_sink() (in module test_boundary_types)
test_find_external_compartment_multi() (in module test_boundary_types)
test_find_external_compartment_single() (in module test_boundary_types)
test_fix_objective_as_constraint() (in module test_solver)
test_fix_objective_as_constraint_minimize() (in module test_solver)
test_fixed_seed() (in module test_sampling)
test_flux_variability() (in module test_variability)
test_flux_variability_benchmark() (in module test_variability)
test_flux_variability_loopless() (in module test_variability)
test_flux_variability_loopless_benchmark() (in module test_variability)
test_format_long_string() (in module test_util)
test_formula_element_setting() (in module test_metabolite)
test_from_sbml_string() (in module test_sbml)
test_fva_data_frame() (in module test_variability)
test_fva_infeasible() (in module test_variability)
test_fva_minimization() (in module test_variability)
test_gapfilling (module)
test_gapfilling() (in module test_gapfilling)
test_gene (module)
test_gene_knock_out() (in module test_core_reaction)
test_gene_knockout() (in module cobra.test.test_manipulation.test_delete)
test_geometric (module)
test_geometric_fba() (in module test_geometric)
test_geometric_fba_benchmark() (in module test_geometric)
test_get_by_any() (in module test_dictlist)
test_get_context() (in module test_context)
test_get_objective_direction() (in module test_model)
test_gpr() (in module test_core_reaction)
test_gpr_modification() (in module test_core_reaction)
test_gprs() (in module test_sbml)
test_group (module)
test_group_add_elements() (in module test_group)
test_group_kind() (in module test_group)
test_group_loss_of_elements() (in module test_model)
test_group_members_add_to_model() (in module test_model)
test_group_model_reaction_association() (in module test_model)
test_groups() (in module test_sbml)
test_history_manager() (in module test_context)
test_iadd() (in module test_core_reaction)
(in module test_dictlist)
test_identifiers_annotation() (in module test_sbml)
test_imap() (in module test_process_pool)
test_imap_unordered() (in module test_process_pool)
test_independent() (in module test_dictlist)
test_index() (in module test_dictlist)
test_inequality_constraint() (in module test_sampling)
test_infinity_bounds() (in module test_sbml)
test_inhomogeneous_sanity() (in module test_sampling)
test_init() (in module test_process_pool)
test_init_copy() (in module test_dictlist)
test_insert() (in module test_dictlist)
test_interface_str() (in module test_solver)
test_invalid_objective_raises() (in module test_model)
test_invalid_solver_change_raises() (in module test_model)
test_io_order (module)
test_io_order() (in module test_io_order)
test_irrev_reaction_set_negative_lb() (in module test_core_reaction)
test_is_boundary_type() (in module test_boundary_types)
test_isub() (in module test_dictlist)
test_json (module)
test_knockout() (in module test_core_reaction)
test_linear_moma_sanity() (in module test_moma)
test_linear_reaction_coefficients() (in module test_solver)
test_load (module)
test_load_json_model() (in module test_json)
test_load_json_model_invalid() (in module test_annotation_format)
test_load_json_model_valid() (in module test_annotation_format)
test_load_matlab_model() (in module test_mat)
test_load_yaml_model() (in module test_yaml)
test_loopless (module)
test_loopless_benchmark_after() (in module test_loopless)
test_loopless_benchmark_before() (in module test_loopless)
test_loopless_pfba_fva() (in module test_variability)
test_loopless_solution() (in module test_loopless)
test_loopless_solution_fluxes() (in module test_loopless)
test_make_irreversible() (in module test_core_reaction)
test_make_irreversible_irreversible_to_the_other_side() (in module test_core_reaction)
test_make_lhs_irreversible_reversible() (in module test_core_reaction)
test_make_reversible() (in module test_core_reaction)
test_map() (in module test_process_pool)
test_map_async() (in module test_process_pool)
test_mass_balance() (in module test_core_reaction)
test_mat (module)
test_merge_models() (in module test_model)
test_metabolite (module)
test_metabolite_formula() (in module test_metabolite)
test_metabolite_summary (module)
test_metabolite_summary_flux_in_context() (in module test_metabolite_summary)
test_metabolite_summary_interface() (in module test_metabolite_summary)
test_metabolite_summary_to_frame() (in module test_metabolite_summary)
test_metabolite_summary_to_html() (in module test_metabolite_summary)
test_metabolite_summary_to_string() (in module test_metabolite_summary)
test_minimal_medium (module)
test_minimal_medium_alternative_mip() (in module test_minimal_medium)
test_minimal_medium_exports() (in module test_minimal_medium)
test_minimal_medium_linear() (in module test_minimal_medium)
test_minimal_medium_linear_benchmark() (in module test_minimal_medium)
test_minimal_medium_mip() (in module test_minimal_medium)
test_minimal_medium_mip_benchmark() (in module test_minimal_medium)
test_minimal_medium_open_exchanges() (in module test_minimal_medium)
test_missing_flux_bounds1() (in module test_sbml)
test_missing_flux_bounds2() (in module test_sbml)
test_model (module)
test_model_from_other_model() (in module test_model)
test_model_history() (in module test_sbml)
test_model_less_reaction() (in module test_core_reaction)
test_model_medium() (in module test_minimal_medium)
test_model_remove_reaction() (in module test_model)
test_model_summary (module)
test_model_summary_flux() (in module test_model_summary)
test_model_summary_flux_in_context() (in module test_model_summary)
test_model_summary_fva() (in module test_model_summary)
test_model_summary_interface() (in module test_model_summary)
test_model_summary_to_frame() (in module test_model_summary)
test_model_summary_to_frame_previous_solution() (in module test_model_summary)
test_model_summary_to_html() (in module test_model_summary)
test_model_summary_to_string() (in module test_model_summary)
test_moma (module)
test_moma_sanity() (in module test_moma)
test_mul() (in module test_core_reaction)
test_multi_optgp() (in module test_sampling)
test_multi_variable_envelope() (in module test_phenotype_phase_plane)
test_no_boundary_reactions() (in module test_boundary_types)
test_no_change_for_same_solver() (in module test_model)
test_no_names_or_boundary_reactions() (in module test_boundary_types)
test_notes (module)
test_notes() (in module test_notes)
test_objective() (in module test_model)
test_objective_coefficient_reflects_changed_objective() (in module test_model)
test_objects_point_to_correct_other_after_copy() (in module test_model)
test_one_left_to_right_reaction_set_positive_ub() (in module test_core_reaction)
test_opposing() (in module test_fastcc)
test_optgp (module)
test_optgp_init_benchmark() (in module test_optgp)
test_optgp_sample_benchmark() (in module test_optgp)
test_optimize() (in module test_model)
test_parallel_flux_variability() (in module test_variability)
test_parsimonious (module)
test_pfba() (in module test_parsimonious)
test_pfba_benchmark() (in module test_parsimonious)
test_pfba_flux_variability() (in module test_variability)
test_phenotype_phase_plane (module)
test_pickle (module)
test_pickle() (in module test_dictlist)
test_problem_properties() (in module test_model)
test_process_pool (module)
test_prune_unused_metabolites_output_type() (in module cobra.test.test_manipulation.test_delete)
test_prune_unused_metabolites_sanity() (in module cobra.test.test_manipulation.test_delete)
test_prune_unused_reactions_output_type() (in module cobra.test.test_manipulation.test_delete)
test_prune_unused_rxns_functionality() (in module cobra.test.test_manipulation.test_delete)
test_q8_consuming_summary() (in module test_metabolite_summary)
test_q8_producing_summary() (in module test_metabolite_summary)
test_query() (in module test_dictlist)
test_radd() (in module test_core_reaction)
test_reaction (module)
test_reaction_bounds_json() (in module test_json)
test_reaction_delete() (in module test_model)
test_reaction_imul() (in module test_core_reaction)
test_reaction_remove() (in module test_model)
test_reaction_summary (module)
test_reaction_summary_flux() (in module test_reaction_summary)
test_reaction_summary_flux_fva() (in module test_reaction_summary)
test_reaction_summary_flux_in_context() (in module test_reaction_summary)
test_reaction_summary_interface() (in module test_reaction_summary)
test_reaction_summary_to_frame() (in module test_reaction_summary)
test_reaction_summary_to_html() (in module test_reaction_summary)
test_reaction_summary_to_string() (in module test_reaction_summary)
test_reaction_without_model() (in module test_core_reaction)
test_read_1() (test_sbml.TestCobraIO method)
test_read_2() (test_sbml.TestCobraIO method)
test_read_pickle() (in module test_pickle)
test_read_sbml_annotations() (in module test_annotation)
test_read_write_sbml_annotations() (in module test_annotation)
test_remote_load() (in module test_load)
test_removal() (in module test_dictlist)
test_removal_from_model_retains_bounds() (in module test_core_reaction)
test_remove_from_model() (in module test_core_reaction)
(in module test_metabolite)
test_remove_gene() (in module test_model)
test_remove_genes() (in module cobra.test.test_manipulation.test_delete)
test_remove_metabolite_destructive() (in module test_model)
test_remove_metabolite_subtractive() (in module test_model)
test_remove_reactions() (in module test_model)
test_rename_genes() (in module cobra.test.test_manipulation.test_modify)
test_repr_html_() (in module test_core_reaction)
(in module test_gene)
(in module test_metabolite)
(in module test_model)
test_reproject() (in module test_optgp)
test_resettable() (in module test_context)
test_room (module)
test_room_sanity() (in module test_room)
test_sampling (module)
test_sampling() (in module test_achr)
(in module test_optgp)
test_save_json_model() (in module test_json)
test_save_matlab_model() (in module test_mat)
test_save_yaml_model() (in module test_yaml)
test_sbml (module)
test_sbo_annotation() (in module cobra.test.test_manipulation.test_annotate)
test_set() (in module test_dictlist)
test_set_bounds_scenario_1() (in module test_core_reaction)
test_set_bounds_scenario_2() (in module test_core_reaction)
test_set_bounds_scenario_3() (in module test_core_reaction)
test_set_bounds_scenario_4() (in module test_core_reaction)
test_set_id() (in module test_metabolite)
test_set_lb_higher_than_ub_sets_ub_to_new_lb() (in module test_core_reaction)
test_set_objective_direction() (in module test_model)
test_set_reaction_objective() (in module test_model)
test_set_reaction_objective_str() (in module test_model)
test_set_ub_lower_than_lb_sets_lb_to_new_ub() (in module test_core_reaction)
test_set_upper_before_lower_bound_to_0() (in module test_core_reaction)
test_show_versions() (in module test_util)
test_single_achr() (in module test_sampling)
test_single_gene_deletion_fba() (in module test_deletion)
test_single_gene_deletion_fba_benchmark() (in module test_deletion)
test_single_gene_deletion_linear_moma() (in module test_deletion)
test_single_gene_deletion_linear_moma_benchmark() (in module test_deletion)
test_single_gene_deletion_linear_room_benchmark() (in module test_deletion)
test_single_gene_deletion_moma() (in module test_deletion)
test_single_gene_deletion_moma_benchmark() (in module test_deletion)
test_single_gene_deletion_moma_reference() (in module test_deletion)
test_single_gene_deletion_room_benchmark() (in module test_deletion)
test_single_optgp() (in module test_sampling)
test_single_point_space() (in module test_sampling)
test_single_reaction_deletion() (in module test_deletion)
test_single_reaction_deletion_benchmark() (in module test_deletion)
test_single_reaction_deletion_linear_room() (in module test_deletion)
test_single_reaction_deletion_room() (in module test_deletion)
test_slice() (in module test_dictlist)
test_slim_optimize() (in module test_model)
test_smbl_with_notes() (in module test_sbml)
test_solution (module)
test_solution_contains_only_reaction_specific_values() (in module test_solution)
test_solution_data_frame() (in module test_model)
test_solver (module)
test_solver() (in module test_configuration)
test_solver_change() (in module test_model)
test_solver_list() (in module test_solver)
test_solver_name() (in module test_solver)
test_sort_and_reverse() (in module test_dictlist)
test_sparse_matrix() (in module test_array)
test_specialized_solver_warning() (in module test_solver)
test_starmap() (in module test_process_pool)
test_starmap_async() (in module test_process_pool)
test_str() (in module test_core_reaction)
test_str_from_model() (in module test_core_reaction)
test_sub() (in module test_core_reaction)
(in module test_dictlist)
test_subtract_metabolite() (in module test_core_reaction)
test_subtract_metabolite_benchmark() (in module test_core_reaction)
test_time_limit() (in module test_solver)
test_tolerance_assignment() (in module test_configuration)
test_toy_model_tolerance_with_different_default() (in module test_configuration)
test_transfer_objective() (in module test_model)
test_twist_irrev_right_to_left_reaction_to_left_to_right() (in module test_core_reaction)
test_union() (in module test_dictlist)
test_unknown_model() (in module test_load)
test_util (module)
test_validate() (in module test_sbml)
,
[1]
test_validate_formula_compartment() (in module cobra.test.test_manipulation.test_validate)
test_validate_json() (in module test_json)
test_validate_mass_balance() (in module cobra.test.test_manipulation.test_validate)
test_validate_wrong_sample() (in module test_achr)
test_validation_warnings() (in module test_sbml)
test_variability (module)
test_variables_samples() (in module test_achr)
(in module test_optgp)
test_weird_left_to_right_reaction_issue() (in module test_core_reaction)
test_with_context() (in module test_process_pool)
test_write_1() (test_sbml.TestCobraIO method)
test_write_2() (test_sbml.TestCobraIO method)
test_write_pickle() (in module test_pickle)
test_wrong_method() (in module test_sampling)
test_yaml (module)
TestCobraIO (class in test_sbml)
tiny_toy_model() (in module cobra.test.conftest)
tmp_path() (in module test_io_order)
to_frame() (cobra.core.Solution method)
(cobra.core.solution.Solution method)
(cobra.Solution method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_html() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_json() (in module cobra.io)
(in module cobra.io.json)
to_string() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_yaml() (in module cobra.io)
(in module cobra.io.yaml)
tolerance (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
tolerance() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
(cobra.summary.Summary property)
(cobra.summary.summary.Summary property)
trial_names (in module test_sbml)
trials (in module test_sbml)
U
Unbounded
UndefinedSolution
undelete_model_genes() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
union() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
Unit (in module cobra.io.sbml)
UNITS_FLUX (in module cobra.io.sbml)
update_costs() (cobra.flux_analysis.gapfilling.GapFiller method)
update_pickles (module)
update_variable_bounds() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
upper_bound (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
upper_bound() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
UPPER_BOUND_ID (in module cobra.io.sbml)
upper_constraint (cobra.util.Components attribute)
(cobra.util.solver.Components attribute)
uppercase_AND (in module cobra.core.reaction)
uppercase_OR (in module cobra.core.reaction)
uptake_flux (cobra.summary.model_summary.ModelSummary attribute)
(cobra.summary.ModelSummary attribute)
url() (cobra.io.AbstractModelRepository property)
(cobra.io.web.abstract_model_repository.AbstractModelRepository property)
(cobra.io.web.AbstractModelRepository property)
URL_IDENTIFIERS_PATTERN (in module cobra.io.sbml)
URL_IDENTIFIERS_PREFIX (in module cobra.io.sbml)
V
validate() (cobra.flux_analysis.gapfilling.GapFiller method)
(cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
validate_sbml_model() (in module cobra.io)
(in module cobra.io.sbml)
variable (cobra.util.Components attribute)
(cobra.util.solver.Components attribute)
variable_bounds (in module cobra.sampling.hr_sampler)
variable_fixed (in module cobra.sampling.hr_sampler)
variables() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
visit_BinOp() (cobra.core.gene.GPRCleaner method)
visit_BoolOp() (cobra.manipulation.delete._GeneRemover method)
visit_Name() (cobra.core.gene.GPRCleaner method)
(cobra.manipulation.delete._GeneRemover method)
(cobra.manipulation.modify._GeneEscaper method)
(cobra.manipulation.modify._Renamer method)
W
warmup (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
weight() (cobra.core.formula.Formula property)
write_sbml_model() (in module cobra.io)
(in module cobra.io.sbml)
X
x (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
x() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
x_dict (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
Y
y (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
y() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Metabolite property)
(cobra.Reaction property)
y_dict (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
yaml (in module cobra.io.yaml)
YAML_SPEC (in module cobra.io.yaml)
Z
ZERO_BOUND_ID (in module cobra.io.sbml)
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